Results 61 to 70 of about 136,245 (330)
Nonequilibrium thermodynamics of non-ideal chemical reaction networks [PDF]
, 2021 All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory that accounts for interactions between chemical species within a mean-field ...
Avanzini F. +3 more
core +1 more source
Robustness of Expressivity in Chemical Reaction Networks [PDF]
, 2016 We show that some natural output conventions for error-free computation in chemical reaction networks (CRN) lead to a common level of computational expressivity. Our main results are that the standard definition of error-free CRNs have equivalent computational power to (1) asymmetric and (2) democratic CRNs.
Robert Brijder +2 more
openaire +3 more sources
Uncertainty-aware prediction of chemical reaction yields with graph neural networks
Journal of Cheminformatics, 2022 In this paper, we present a data-driven method for the uncertainty-aware prediction of chemical reaction yields. The reactants and products in a chemical reaction are represented as a set of molecular graphs.
Youngchun Kwon +3 more
doaj +1 more source
Efficient simulation of stochastic chemical kinetics with the Stochastic Bulirsch-Stoer extrapolation method [PDF]
, 2014 BackgroundBiochemical systems with relatively low numbers of components must be simulated stochastically in order to capture their inherent noise. Although there has recently been considerable work on discrete stochastic solvers, there is still a need ...
Barrio Solórzano, Manuel +11 more
core +1 more source
Diffusive network connected chemical reaction networks
Systems Science & Control EngineeringA novel type of networked Chemical Reaction Network (CRN) model is proposed in this paper where the CRN subsystem nodes are connected in a bi-directional state-difference-driven way, forming a diffusive network. The diffusive connecting elements can also
Katalin M. Hangos +2 more
doaj +1 more source
Compilation and Inference with Chemical Reaction Networks [PDF]
, 2022 The successful advancement and deployment of technologies in the field of synthetic biology will require sophisticated computational infrastructure coupled with new theoretical ideas in order to more effectively engineer and reverse engineer biochemical ...
Poole, William
core +1 more source
Translated Chemical Reaction Networks
Bulletin of Mathematical Biology, 2014 Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polynomial ordinary differential equations.
openaire +4 more sources
Bayesian Verification of Chemical Reaction Networks [PDF]
, 2020 We present a data-driven verification approach that determines whether or not a given chemical reaction network (CRN) satisfies a given property, expressed as a formula in a modal logic. Our approach consists of three phases, integrating formal verification over models with learning from data.
Gareth W. Molyneux +2 more
openaire +2 more sources
Law of Localization in Chemical Reaction Networks
Physical Review Letters, 2016 18 pages 5 figures; v2: minor corrections (accepted for publication in Physical Review Letters)
Okada, Takashi, Mochizuki, Atsushi
openaire +4 more sources
Reaction networks as systems for resource allocation: a variational principle for their non-equilibrium steady states. [PDF]
PLoS ONE, 2012 Within a fully microscopic setting, we derive a variational principle for the non-equilibrium steady states of chemical reaction networks, valid for time-scales over which chemical potentials can be taken to be slowly varying: at stationarity the system ...
Andrea De Martino +3 more
doaj +1 more source